PDFhandler is confirmed installed on Special:Versions, which returns all the required directories, and no extensions could be interfering with the install. What's the issue?
Topic on Extension talk:PdfHandler
I am having this issue too. I have changed the settings in ImageMagick so that PDFs are able to be converted; verified this at the command line; verified that all 4 related utilities are working at the command line; run all the maintenance scripts; and...nothing.
..check /etc/ImageMagick-<your_version>/policy.xml
if <policy domain="coder" rights="none" pattern="PDF" /> means convert is not allowed to perform its job..
you might change rights="read | write"
but you should be aware and responsible of the security risks this might bring (check post below from Cbolts)